This is a generated RPPA Report generated from the following scripts,

-Pathway_Score_calculator.ipynb - Score_Caluclator.Rmd (eventually this will be encorporated into the Pathway_Score_calculator.ipynb) -Pathway_Score_calculator.ipynb -Pathway_prepare_Density_maper.Rmd -Heat_mapper.Rmd -RPPA_Report.Rmd

All Scripts must be run prior to running this script or it will not work,Knit this file together and a HTML report will be generated if you wish to change the format of this file you may alter HTML instructions.

This is the report file for Patient ______

packages and data read in

First Lets take a look at the pathway Scores

Lets look at the pathway scoring

kbl(Pathway_key, booktabs = T)
Pathway Predictor Weight Count
2 Apoptosis CASPASE7CLEAVEDD198 1 1
3 Apoptosis Caspase-8 1 1
4 Apoptosis Caspase_3_cleaved 1 1
5 BH3_Balance BAK 1 1
6 BH3_Balance BAX 1 1
7 BH3_Balance BID 1 1
8 BH3_Balance BIM 1 1
9 BH3_Balance MCL-1 -1 1
10 BH3_Balance BADPS112 -1 1
11 BH3_Balance BCL2 -1 1
12 BH3_Balance BCLXL -1 1
13 BH3_Balance CIAP2 -1 1
14 Cell_cycle_progression Cyclin-B1 1 1
15 Cell_cycle_progression PLK1 1 1
16 Cell_cycle_progression CDK1_pT14 1 1
17 Cell_cycle_progression Chk1 1 1
18 Cell_cycle_progression cdc25C 1 1
19 Cell_cycle_progression Rb_pS807_S811 1 1
20 Cell_cycle_progression p21 -1 1
21 Cell_cycle_progression p27_pT198 -1 1
22 Cell_cycle_progression CyclinD1 -1 1
23 Cell_cycle_progression 1433BETA -1 1
24 DNA_Damage Histone-H3 1 1
25 DNA_Damage H2AX_pS139 1 1
26 DNA_Damage H2AX_pS140 1 1
27 DNA_Damage_Checkpoint ATM_pS1981 1 1
28 DNA_Damage_Checkpoint ATR_pS428 1 1
29 DNA_Damage_Checkpoint CDK1_pY15 1 1
30 DNA_Damage_Checkpoint Chk1_pS296 1 1
31 DNA_Damage_Checkpoint Chk2_pT68 1 1
32 DNA_Damage_Checkpoint Wee1_pS642 1 1
33 G0_G1 1433BETA 1 1
34 G0_G1 53BP1 1 1
35 G0_G1 BRD4 -1 1
36 G0_G1 Cyclin-D1 1 1
37 G0_G1 Cyclin-B1 -1 1
38 G0_G1 p27_pT198 1 1
39 G0_G1 p21 1 1
40 G1_S 53BP1 1 1
41 G1_S BRD4 1 1
42 G1_S Cyclin-E1 1 1
43 G2_M Cyclin-B1 1 1
44 G2_M PLK1 1 1
45 G2_M CDK1_pT14 1 1
46 G2_M cdc25C 1 1
47 G2_M Rb_pS807_S811 1 1
48 Hormone_receptor ERALPHA 1 1
49 Hormone_receptor PR 1 1
50 Hormone_receptor AR 1 1
51 Hormone_signaling_Breast GATA3 1 1
52 Hormone_signaling_Breast BCL2 1 1
53 Hormone_signaling_Breast ERALPHA_pS118 1 1
54 Immune Lck 1 1
55 Immune ZAP-70 1 1
56 Immune CD4 1 1
57 Immune CD45 1 1
58 Immune_Checkpoint B7-H4 1 1
59 Immune_Checkpoint PD-L1 1 1
60 Immune_Checkpoint PD-1 1 1
61 Immune_Checkpoint B7-H3 1 1
62 Notch Jagged1 1 1
63 Notch Notch3 1 1
64 Notch TAZ 1 1
65 Notch YAP 1 1
66 Notch YAP_pS127 -1 1
67 PI3K_Akt Akt_pS473 0.5 0.5
68 PI3K_Akt Akt_pT308 0.5 0.5
69 PI3K_Akt GSK3ALPHABETA_pS21S9 1 1
70 PI3K_Akt p27_pT198 1 1
71 PI3K_Akt PRAS40_pT246 1 1
72 PI3K_Akt PTEN -1 1
73 RAS_MAPK B-Raf_pS445 1 1
74 RAS_MAPK c-Jun_pS73 1 1
75 RAS_MAPK C-Raf_pS338 1 1
76 RAS_MAPK MEK1_p_S217-S221 1 1
77 RAS_MAPK P38_pT180Y182 1 1
78 RAS_MAPK p90RSK_pT573 1 1
79 RAS_MAPK YB1_pS102 1 1
80 RAS_MAPK MAPK_pT202Y204 1 1
81 RTK CMET_pY1235 1 1
82 RTK EGFR_pY1173 1 1
83 RTK HER2_pY1248 1 1
84 RTK HER3_pY1289 1 1
85 RTK IGF1R_pY1135_Y1136 1 1
86 RTK IRS1 1 1
87 RTK Src_pY527 1 1
88 RTK SHP-2_pY542 1 1
89 RTK Shc_pY317 1 1
90 RTK Src_pY416 1 1
91 TSC_mTOR 4E-BP1_pS65 1 1
92 TSC_mTOR mTOR_pS2448 1 1
93 TSC_mTOR p70-S6K_pT389 1 1
94 TSC_mTOR Rb_pS807_S811 1 1
95 TSC_mTOR Rictor_pT1135 1 1
96 TSC_mTOR S6_pS235_S236 0.5 0.5
97 TSC_mTOR S6_pS240_S244 0.5 0.5
98 Tumor_Content BETACATENIN 1 1
99 Tumor_Content Claudin-7 1 1
100 Tumor_Content E-Cadherin 1 1
101 Tumor_Content RBM15 1 1
102 Tumor_Content EPPK1 1 1
103 Tumor_Content Caveolin-1 -1 1
104 Tumor_Content Collagen-VI -1 1
105 Tumor_Content Lck -1 1
106 Tumor_Content MMP2 -1 1
107 Tumor_Content PAI-1 -1 1
108 Histone_Alteration DM_Histone_H3 1 1
109 Histone_Alteration DM_K9_Histone_H3 1 1
110 Histone_Alteration U_Histone_H2B 1 1
111 RPA32_pS4_S8 RPA32_pS4_S8 1 1
112 RRM1 RRM1 1 1
113 RRM2 RRM2 1 1
114 JAK-STAT STAT3_pY705 1 1
115 JAK-STAT STAT5ALPHA 1 1
116 JAK-STAT JAK2 1 1
117 Epigenetic DNMT1 1 1
118 Epigenetic ARID1A 1 1
119 Epigenetic BRD4 1 1

Now lets look at the the proteins that were dropped from the Pathways analysis

The following samples are missing

#Our Sample Patient ______ is missing

#This part will need to be altered depending on our patient of intrest
Missing_Sample_for_Our_patient<-Missing_Samples%>%filter(Sample=="261035")
reactable(Missing_Sample_for_Our_patient)

Sepcifically it is missing the following proteins

Missing_Proteins_Full<-Missing_Proteins_Full%>%select(Predictor,"261035")#THIS NEEDS TO BE ALTERED TO DISIRED SAMPLE OR SAMPLES

proteins<-Missing_Proteins_Full[is.na(Missing_Proteins_Full$`261035`),]

reactable(proteins)

The Following Proteins are missing

We can also visualize the missing proteins in histograms to make it more understandable #There was ____ Samples with a largen than normal missing amount of proteins these were removed and the graph was remade for visability purposes

#This section is going to have to be used on a case by case basis bedpending on how many missing samples are present 
Missing_Proteins2<-Missing_Proteins%>%filter(Protein != "CASPASE3CLEAVED")
col2<-ggplot(Missing_Proteins2, aes(Protein,Amount_Missing,fill=Protein))+geom_col()+theme_classic()+ ggtitle("Missing Proteins By Amount Missing")+ theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ theme(legend.position="none")

col2

Density graphs

#Heat Maps

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